Function type overview
Function in Spectre are grouped by the function prefix:
| Prefix | Description |
|---|---|
| package. | Functions that relate to managing the Spectre package and related dependencies. e.g. package.check(). |
| read. | Functions that read files into R. e.g. read.files(). |
| do. | Functions that manipulate or modify data, such as filtering or subsampling. e.g. do.subsample(). |
| run. | Functions that run an analytical process, such as FlowSOM or UMAP. e.g. run.umap(). |
| make. | Functions that create a data or visual output that is saved to disk. e.g. make.colour.plot(). |
| write. | Functions that write data to disk. e.g. write.files(). |
Spectre and other package loading/management
| Task | Command (with minimum variable inputs) |
|---|---|
| Load Spectre and other packages | ## Load Spectre library(Spectre) ## Check if required packages are loaded Spectre::package.check() ## Load required packages Spectre::package.load() |
| Set working directory to the location of your script, and saves this location as 'PrimaryDirectory' | ### Set working directory dirname(rstudioapi::getActiveDocumentContext()$path) # Finds the directory where this script is located setwd(dirname(rstudioapi::getActiveDocumentContext()$path)) # Sets the working directory to where the script is located getwd() PrimaryDirectory <- getwd() PrimaryDirectory |
